The first one is indeed a feature without phylum level classification (and the command I provided to you removes them). The second one is a feature that is actually classified at the phylum level, but it doesn't have a name. You can read more about this in this post.
If you also want to get rid of those, one idea that comes to my mind is to use RESCRIPt first to edit the taxonomy:
qiime rescript edit-taxonomy \
--i-taxonomy my_taxonomy.qza \
--p-search-strings p__; \
--p-replacement-strings p__ExcludeMe; \
--o-edited-taxonomy my_taxonomy_edited.qza
And then exclude them directly with another qiime taxa filter-table (this time using --p-exclude):
qiime taxa filter-table \
--i-table filtered_table.qza \
--i-taxonomy my_taxonomy_edited.qza \
--p-exclude p__ExcludeMe \
--p-mode contains \
--o-filtered-table double_filtered_table.qza
Best,
Sergio